Biology subjects

Vicentini, R.

Publications and source records attributed to Vicentini, R..

5 recordsLinked to original sources

bioRxiv2025

Characterization of new thermophilic antibiotic resistance markers

The genetic engineering of thermophilic bacteria is constrained by limited availability of thermostable antibiotic resistance markers for selection. Clostridium thermocellum, a promising candidate for consolidated bioprocessing of lignocellulosic biomass, requires reliable selection systems that function at elevated temperatures. Here, we systematically evaluated antibiotic susceptibility profiles and identified novel resistance markers for this thermophile through bioinformatic screening and experimental validation. We screened 823 thermophilic genomes against the Comprehensive Antibiotic Resistance Database, identifying 1,115 antibiotic resistance genes. From these, we selected candidates with highest homology to resistance determinants for rifampicin, tetracycline, erythromycin, thiamphenicol, and neomycin. We identified three novel antibiotic resistance systems that function in this organism: tetracycline/tet(45), erythromycin/cmeC, and rifampicin/rbpA. Of these, the rifampicin/rbpA provided the highest selection range , > 10,000-fold. Our results establish rbpA as an outstanding selectable marker for thermophilic genetic engineering and provide a validated workflow for discovering thermostable resistance determinants in high-temperature microorganisms. ImportanceThermophilic bacteria like Clostridium thermocellum hold tremendous potential for sustainable biofuel production from plant biomass, but their genetic manipulation has been severely limited by the lack of selection markers that work at high temperatures. Many existing antibiotic resistance systems do not function at thermophilic temperatures, and many approaches to genetic manipulation require multiple antibiotic resistance markers. Currently only two markers are available for C. thermocellum, and only one (cat) functions well. The newly-developed rbpA marker functions well in C. thermocellum and is likely to provide dramatic new opportunities for engineering thermophilic host organisms.

microbiology↗

bioRxiv2025

First chromosome scale genome of Acrocomia aculeata

The Arecaceae family comprises economically, and ecologically significant palm species widely distributed across tropical and subtropical regions. Among them, Acrocomia aculeata, commonly known as Macauba, has gained attention due to its high oil yield, environmental adaptability, and potential applications in sustainable agriculture and bioenergy production. This study presents the first chromosome scale genome assembly of A. aculeata and the first reference genome of the genus, using Oxford Nanopore Technologies sequencing, PacBio HiFi and Hi-C proximity ligation data. The genome covers 1.94 Gbp in the 15 pseudochromosomes, with N50 of 143.43 Mbp, achieving a base quality (QV) of 76.4 and a k-mer completeness of 90.58% of PacBio HiFi data, with k=21. Interspersed repetitive regions represent 77.36% of the total genome, with long terminal repeat (LTRs) accounting for 54.98%. A total of 28.215 protein-coding genes were predicted. The genome was validated with BUSCO, achieving a completeness of 98.9% for predicted proteins. The first chromosome scale genome of Macauba provide new insights and breakthroughs for studies of conservation genomics and plant breeding programs.

genomics↗

bioRxiv2024

Identifying Candidate Genes for Sugar Accumulation in Sugarcane Cultivars: From a Syntenic Genomic Region to a Gene Coexpression Network

Elucidating the intricacies of the sugarcane genome is essential for breeding superior cultivars. This economically important crop originates from hybridizations of highly polyploid Saccharum species. However, the large size (10 Gb), high polyploidy, and aneuploidy of the sugarcane genome pose significant challenges to complete genome sequencing, assembly, and annotation. One successful strategy for identifying candidate genes linked to agronomic traits, particularly those associated with sugar accumulation, leverages synteny and potential collinearity with related species. In this study, we explored synteny between sorghum and sugarcane. Genes from a sorghum Brix QTL were used to screen bacterial artificial chromosome (BAC) libraries from two Brazilian sugarcane varieties (IACSP93-3046 and SP80-3280). The entire region was successfully recovered, confirming synteny and collinearity between the species. Manual annotation identified 51 genes in the hybrid varieties that were subsequently confirmed to be present in Saccharum spontaneum. To identify candidate genes for sugar accumulation, this study employed a multifaceted approach, including retrieving the genomic region of interest, performing gene-by-gene analysis, analyzing RNA-seq data of internodes from Saccharum officinarum and S. spontaneum accessions, constructing a coexpression network to examine the expression patterns of genes within the studied region and their neighbors, and finally identifying differentially expressed genes (DEGs). This comprehensive approach led to the discovery of three candidate genes potentially involved in sugar accumulation: an ethylene-responsive transcription factor (ERF), an ABA 8-hydroxylase, and a prolyl oligopeptidase (POP). These findings could be valuable for identifying additional candidate genes for other important agricultural traits and directly targeting candidate genes for further work in molecular breeding.

genomics↗

bioRxiv2023

Regulation of PYR/PYL/RCAR ABA receptors mRNA stability: involvement of miR5628 in decay of PYL6 mRNA

Hormone signaling fine-tuning involves feedback regulatory loops. Abscisic acid (ABA) plays key functions in development and tolerance to abiotic stress. ABA is sensed by the PYR/PYL/RCAR receptors and it also represses their gene expression. Conversely, ABA induces PP2C phosphatases expression, which are negative regulators of the ABA signaling pathway. This feedback regulatory scheme is likely important for the modulation of ABA signal transduction. Here, we provide a new insight into the mechanisms underlying the ABA-induced negative control of PYR/PYL/RCAR expression in Arabidopsis thaliana. The strong and sustained repression of PYR/PYL/RCARs revealed by ABA time course treatment defines the regulation of receptors genes as an important step in resetting the ABA signaling pathway. Transcription inhibition by cordycepin showed that destabilization of PYL1/4/5/6 mRNA is involved in ABA-induced repression of these genes. Furthermore, genetic evidence indicated that decapping may play a role in PYL4/5/6 mRNAs decay. In addition, we provide evidence that the Arabidopsis-specific microRNA5628 (miR5628), which is transiently induced by the ABA core signaling pathway, guides the cleavage of PYL6 transcript in response to ABA. After cleavage, the resulting RISC 5- and 3-cleaved fragments of PYL6 mRNA may be degraded by exoribonuclease XRN4. MiR5628 is an evolutionary novelty that may contribute, with decapping and XRN4 activities, to enhance PYL6 mRNA degradation. Thus, control of stability of PYR/PYL/RCAR transcripts is an important step in maintaining homeostasis of ABA signaling. One Sentence SummaryAttenuation of ABA signaling involves destabilization of PYL1/4/5/6 transcripts. ABA core signaling induces miR5628 expression to enhance PYL6 mRNA degradation in conjunction with decapping and XRN4 activities.

plant biology↗

bioRxiv2018

Genetic variation in a complex polyploid: unveiling the dynamic allelic features of sugarcane

BackgroundSugarcane (Saccharum spp.) is highly polyploid and aneuploid. Modern cultivars are derived from hybridization between S. officinarum and S. spontaneum. This combination results in a genome exhibiting variable ploidy among different loci, a huge genome size (approximately 10 Gb) and a high content of repetitive regions. Gene expression mechanisms are poorly understood in these cultivars. An approach using genomic, transcriptomic and genetic mapping can improve our knowledge of the behavior of genetics in sugarcane.\n\nResultsThe hypothetical HP600 and centromere protein C (CENP-C) genes from sugarcane were used to elucidate the allelic expression and genomic and genetic behavior of this complex polyploid. The genomically side-by-side genes HP600 and CENP-C were found in two different homeologous chromosome groups with ploidies of eight and ten. The first region (Region01) was a Sorghum bicolor ortholog with all haplotypes of HP600 and CENP- C expressed, but HP600 exhibited an unbalanced haplotype expression. The second region (Region02) was a scrambled sugarcane sequence formed from different noncollinear genes containing duplications of HP600 and CENP-C (paralogs). This duplication occurred before the Saccharum genus formation and after the separation of sorghum and sugarcane, resulting in a nonexpressed HP600 pseudogene and a recombined fusion version of CENP-C and orthologous gene Sobic.003G299500 with at least two chimerical gene haplotypes expressed. The genetic map construction supported the difficulty of mapping markers located in duplicated regions of complex polyploid genomes.\n\nConclusionAll these findings describe a low synteny region in sugarcane, formed by events occurring in all members of the Saccharum genus. Additionally, evidence of duplicated and truncate gene expression and the behavior of genetic markers in a duplicated region was found. Thus, we describe the complexity involved in sugarcane genetics and genomics and allelic dynamics, which can be useful for understanding the complex polyploid genome.

plant biology↗